ArticleGenome biology2008
Sequence-based prediction of protein-protein interactions by means of codon usage.
Article in Genome biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Predicting Protein-Protein Interactions by Convolutional Neural Network Model.Biotech (Basel (Switzerland)) · 2026Article
- Protein-protein interaction and non-interaction predictions using gene sequence natural vector.Communications biology · 2022Article
- Computational models for prediction of protein-protein interaction in rice andFrontiers in plant science · 2022Article
- A scheme for inferring viral-host associations based on codon usage patterns identifies the most affected signaling pathways during COVID-19.Journal of biomedical informatics · 2021Article
- Using discriminative vector machine model with 2DPCA to predict interactions among proteins.BMC bioinformatics · 2019Article
- Computational identification of protein-protein interactions in model plant proteomes.Scientific reports · 2019Article
- A novel matrix of sequence descriptors for predicting protein-protein interactions from amino acid sequences.PloS one · 2019Article
- PCVMZM: Using the Probabilistic Classification Vector Machines Model Combined with a Zernike Moments Descriptor to Predict Protein-Protein Interactions from Protein Sequences.International journal of molecular sciences · 2017Article
- Improved protein-protein interactions prediction via weighted sparse representation model combining continuous wavelet descriptor and PseAA composition.BMC systems biology · 2016Article
- Prediction of Protein-Protein Interactions by Evidence Combining Methods.International journal of molecular sciences · 2016Review
- Improving protein-protein interactions prediction accuracy using protein evolutionary information and relevance vector machine model.Protein science : a publication of the Protein Society · 2016Article
- The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function.Journal of molecular evolution · 2016Review
- Bicluster pattern of codon context usages between flavivirus and vector mosquito Aedes aegypti: relevance to infection and transcriptional response of mosquito genes.Molecular genetics and genomics : MGG · 2014Article
- A novel feature extraction scheme with ensemble coding for protein-protein interaction prediction.International journal of molecular sciences · 2014Article
- Computational prediction of the human-microbial oral interactome.BMC systems biology · 2014Article
- Unraveling patterns of site-to-site synonymous rates variation and associated gene properties of protein domains and families.PloS one · 2014Article
- ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants.Plant & cell physiology · 2014Article
- Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources.Current genomics · 2013Article
- The relation of codon bias to tissue-specific gene expression in Arabidopsis thaliana.Genetics · 2012Article
- Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs.BMC bioinformatics · 2012Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We introduce a novel approach to predict interaction of two proteins solely by analyzing their coding sequences. We found that similarity in codon usage is a strong predictor of protein-protein interactions and, for high specificity values, is as sensitive as the most powerful current prediction methods. Furthermore, combining codon usage with other predictors results in a 75% increase in sensitivity at a precision of 50%, compared to prediction without considering codon usage.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.